2IBS

Crystal structure of the adenine-specific DNA methyltransferase M.TaqI complexed with the cofactor analog AETA and a 10 bp DNA containing 2-aminopurine at the target position


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.195 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

2-Aminopurine Flipped into the Active Site of the Adenine-Specific DNA Methyltransferase M.TaqI: Crystal Structures and Time-Resolved Fluorescence

Lenz, T.Bonnist, E.Y.M.Pljevaljcic, G.Neely, R.K.Dryden, D.T.F.Scheidig, A.J.Jones, A.C.Weinhold, E.

(2007) J.Am.Chem.Soc. 129: 6240-6248

  • DOI: 10.1021/ja069366n
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • We report the crystal structure of the DNA adenine-N6 methyltransferase, M.TaqI, complexed with DNA, showing the fluorescent adenine analog, 2-aminopurine, flipped out of the DNA helix and occupying virtually the same position in the active site as t ...

    We report the crystal structure of the DNA adenine-N6 methyltransferase, M.TaqI, complexed with DNA, showing the fluorescent adenine analog, 2-aminopurine, flipped out of the DNA helix and occupying virtually the same position in the active site as the natural target adenine. Time-resolved fluorescence spectroscopy of the crystalline complex faithfully reports this state: base flipping is accompanied by the loss of the very short ( approximately 50 ps) lifetime component associated with fully base-stacked 2-aminopurine in DNA, and 2-aminopurine is subject to considerable quenching by pi-stacking interactions with Tyr108 in the catalytic motif IV (NPPY). This proves 2-aminopurine to be an excellent probe for studying base flipping by M.TaqI and suggests similar quenching in the active sites of DNA and RNA adenine-N6 as well as DNA cytosine-N4 methyltransferases sharing the conserved motif IV. In solution, the same distinctive fluorescence response confirms complete destacking from DNA and is also observed when the proposed key residue for base flipping by M.TaqI, the target base partner thymine, is substituted by an abasic site analog. The corresponding cocrystal structure shows 2-aminopurine in the active site of M.TaqI, demonstrating that the partner thymine is not essential for base flipping. However, in this structure, a shift of the 3' neighbor of the target base into the vacancy left after base flipping is observed, apparently replicating a stabilizing role of the missing partner thymine. Time-resolved fluorescence and acrylamide quenching measurements of M.TaqI complexes in solution provide evidence for an alternative binding site for the extra-helical target base within M.TaqI and suggest that the partner thymine assists in delivering the target base into the active site.


    Related Citations: 
    • Differential binding of S-adenosylmethionine S-adenosylhomocysteine and Sinefungin to the adenine-specific DNA methyltransferase M.TaqI
      Schluckebier, G.,Kozak, M.,Bleimling, N.,Weinhold, E.,Saenger, W.
      (1997) J.Mol.Biol. 265: 56
    • Structure of the N6-adenine DNA methyltransferase M.TaqI in complex with DNA and a cofactor analog
      Goedecke, K.,Pignot, M.,Goody, R.S.,Scheidig, A.J.,Weinhold, E.
      (2001) Nat.Struct.Mol.Biol. 8: 121


    Organizational Affiliation

    Institute of Organic Chemistry, RWTH Aachen University, Landoltweg 1, D-52056 Aachen, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Modification methylase TaqI
A, D
421Thermus aquaticusMutation(s): 0 
Gene Names: taqIM
EC: 2.1.1.72
Find proteins for P14385 (Thermus aquaticus)
Go to UniProtKB:  P14385
Entity ID: 1
MoleculeChainsLengthOrganism
5'-D(*GP*TP*TP*CP*GP*(2PR)P*TP*GP*TP*C)-3'B,E10N/A
Entity ID: 2
MoleculeChainsLengthOrganism
5'-D(*GP*AP*CP*AP*TP*CP*GP*(6MA)P*AP*C)-3'C,F10N/A
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NEA
Query on NEA

Download SDF File 
Download CCD File 
A, D
5'-DEOXY-5'-[2-(AMINO)ETHYLTHIO]ADENOSINE
C12 H18 N6 O3 S
APAPOJUCRZTCHD-WOUKDFQISA-N
 Ligand Interaction
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
6MA
Query on 6MA
C, F
DNA LINKINGC11 H16 N5 O6 PA
2PR
Query on 2PR
B, E
DNA LINKINGC10 H14 N5 O6 PDG
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
NEAKd: 500 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.195 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 59.530α = 90.00
b = 69.160β = 92.18
c = 114.640γ = 90.00
Software Package:
Software NamePurpose
MAR345data collection
REFMACrefinement
ProDCdata collection
XDSdata scaling
CNSphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2007-05-29
    Type: Initial release
  • Version 1.1: 2008-05-01
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2017-10-18
    Type: Refinement description